Huntington?s disease (HD), one of the first neurodegenerative diseases for which a genetic cause was determined, is an inherited neurodegenerative disorder that has no disease-modifying treatment. HD is caused by a CAG repeat expansion in the HTT gene encoding a polyglutamine (polyQ) tract within the amino terminal portion of Huntingtin (HTT). While the field has gained an understanding of the many cellular processes that are disrupted in HD, we do not yet understand the interplay between key proximal HD-associated events, such as the relationship between aberrant mutant HTT (mHTT) accumulation, RNA biology and epigenetic events in specific cell types in the brain. Similarly, we do not know how changes in these processes impact clinical manifestation of disease, where best to intervene therapeutically and what outcome measures may be the most informative in HD models. The overarching focus of the research proposed here is to fill vital gaps in our knowledge about how these factors impact onset and progression of HD and how that understanding might lead to new disease-altering therapies. The proposed research will leverage unique resources and methods developed in my lab and those of my collaborators and will utilize state-of-the-art technologies such as single-cell RNA-seq, mass spectrometry and cryo-electron tomography to dissect molecular mechanisms. Ultimately, treatments for this disease, including combination therapies, will likely require a much better fundamental understanding of how mHTT leads to HD pathology and death. Our recent data suggests unexpected relationships between protein posttranslational modification (PTM) pathways, aberrant mutant HTT accumulation and DNA damage responses in neurons, the latter now implicated as a critical modifier of HD age-of-onset. Using a systems biology approach we are learning how chronic expression and accumulation of mHTT impacts gene expression and now seek to develop a more comprehensive understanding of RNA biology and causal networks in specific cell types. Here I propose investigations aimed at addressing major gaps in our understanding of how the fundamental molecular and cellular events underlie how the mutant HD gene causes degeneration of specific cell populations in the brain to induce motor and cognitive decline and ultimately premature death of patients. My program benefits from the integrated use of patient iPSCs and HD mouse models and the extensive and productive collaborations we have established over many years. With the overall goal of understanding proximal and initiating events in the disease and developing therapies for HD, I propose two primary avenues of research relating to the integration of 1) protein homeostasis and 2) epigenetics and RNA biology in HD.